atoms.center()
pl_atoms1 = range(4)
pl_atoms2 = range(8, 12)
pl_cell1 = (L, L, 4 * a)
pl_cell2 = pl_cell1
t = Transport(h=0.3,
xc='LDA',
basis={'Na': basis},
kpts=(1,1,1),
occupations=FermiDirac(0.1),
mode='lcao',
poissonsolver=PoissonSolver(nn=2, relax='GS'),
txt='Na_lcao.txt',
mixer=Mixer(0.1, 5, weight=100.0),
guess_steps=10,
fix_contour=True,
pl_atoms=[pl_atoms1, pl_atoms2],
pl_cells=[pl_cell1, pl_cell2],
pl_kpts=(1,1,16),
fixed_boundary=False,
analysis_data_list=['tc'],
edge_atoms=[[0, 3], [0, 11]],
mol_atoms=range(4, 8))
atoms.set_calculator(t)
t.calculate_to_bias(0.0, 1)
qn=QuasiNewton(atoms, trajectory='transport.traj')
qn.run(fmax=0.05)
atoms.positions[:, :2] = L / 2.
atoms.center()
pl_atoms1 = range(4)
pl_atoms2 = range(8, 12)
pl_cell1 = (L, L, 4 * a)
pl_cell2 = pl_cell1
t = Transport(h=0.3,
xc='LDA',
basis={'Na': basis},
kpts=(1, 1, 1),
occupations=FermiDirac(0.1),
mode='lcao',
poissonsolver=PoissonSolver(nn=2, relax='GS'),
txt='Na_lcao.txt',
mixer=Mixer(0.1, 5, weight=100.0),
guess_steps=10,
fix_contour=True,
pl_atoms=[pl_atoms1, pl_atoms2],
pl_cells=[pl_cell1, pl_cell2],
pl_kpts=(1, 1, 16),
fixed_boundary=False,
analysis_data_list=['tc'],
edge_atoms=[[0, 3], [0, 11]],
mol_atoms=range(4, 8))
atoms.set_calculator(t)
t.calculate_to_bias(0.0, 1)
qn = QuasiNewton(atoms, trajectory='transport.traj')
qn.run(fmax=0.05)
